I went to Set defaults for conversion - Chapter Detection - and selected the box Add chapters to table of contents

I hit okay, then turned of Calibre and restarted it again. In the preferences it shows the box check marked but when I go to convert a story it's not check marked anymore.

Also, for the one file I converted I got two chapter 1's, two chapter 2s and so on...I'm not sure if that's related to this or not?

EDIT: I did a test and for some reason anything tagged <H2>Chapter </H2> has a double entry in the TOC. The other story that does not have traditional Chapter headers but instead uses Days is displaying correctly.

Changing the defaults does not affect the setting for files you've previously converted. Only the settings for new conversions. The idea being that when you convert a file, the settings you used for that file are saved and override the default.

Changing the defaults does not affect the setting for files you've previously converted. Only the settings for new conversions. The idea being that when you convert a file, the settings you used for that file are saved and override the default.

ah, I think I see. So basically this doesn't affect why I'm getting two chapter posts per chapter on the table of contents...